NAME

       Bio::MapIO::fpc - A FPC Map reader

SYNOPSIS

       # do not use this object directly it is accessed through the Bio::MapIO system

           use Bio::MapIO;

            -format  : specifies the format of the file format is "fpc",
            -file    : specifies the name of the .fpc file
            -readcor : boolean argument, indicating if .cor is to be read
                        or not. It looks for the .cor file in the same path
                        as .fpc file.
                        0 : doesn't read .cor file
                        1 : reads the .cor file
                        [default 0]
            -verbose : indicates the process of loading of fpc file
           my $mapio = Bio::MapIO->new(-format  => "fpc",
                                      -file    => "rice.fpc",
                                      -readcor => 0,
                                      -verbose => 0);

           my $map = $mapio->next_map();

           foreach my $marker ( $map->each_markerid() ) {
                # loop through the markers associated with the map
                # likewise for contigs, clones, etc.
           }

DESCRIPTION

       This object contains code for parsing and processing FPC files and creating
       Bio::Map::Physical object from it.

       For faster access and better optimization, the data is stored internally in hashes. The
       corresponding objects are created on request.

       We handle reading of the FPC ourselves, since MapIO module of Bioperl adds too much
       overhead.

Initializer

   _initialize
        Title   : _initialize
        Usage   : called implicitly
        Function: calls the SUPER::_initialize
        Returns : nothing
        Args    : species, readcor

Access Methods

       These methods let you get and set the member variables

   next_map
        Title   : next_map
        Usage   : my $fpcmap = $mapio->next_map();
        Function: gets the fpcmap from MapIO
        Returns : object of type L<Bio::Map::MapI>
        Args    : none

   write_map
        Title   : write_map
        Usage   : $mapio->write_map($map);
        Function: Write a map out
        Returns : none
        Args    : Bio::Map::MapI

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Gaurav Gupta

       Email gaurav@genome.arizona.edu

PROJECT LEADERS

       Jamie Hatfield            jamie@genome.arizona.edu

       Dr. Cari Soderlund        cari@genome.arizona.edu

PROJECT DESCRIPTION

       The project was done in Arizona Genomics Computational Laboratory (AGCoL) at University of
       Arizona.

       This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for the Computation
       and Display of Physical Mapping Data".

       For more information on this project, please refer:
         http://www.genome.arizona.edu

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _